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- EMDB-66968: The focused structure of the N-terminal lobe of the human UBR4 -

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Basic information

Entry
Database: EMDB / ID: EMD-66968
TitleThe focused structure of the N-terminal lobe of the human UBR4
Map data
Sample
  • Complex: N-terminal lobe of the human UBR4
    • Protein or peptide: E3 ubiquitin-protein ligase UBR4
KeywordsUbiquitinalytion / LIGASE
Function / homology
Function and homology information


negative regulation of HRI-mediated signaling / ubiquitin-dependent protein catabolic process via the N-end rule pathway / HRI-mediated signaling / cytoplasm protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / negative regulation of fatty acid biosynthetic process / endosome organization / cytoplasm protein quality control / protein K11-linked ubiquitination / protein K27-linked ubiquitination ...negative regulation of HRI-mediated signaling / ubiquitin-dependent protein catabolic process via the N-end rule pathway / HRI-mediated signaling / cytoplasm protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / negative regulation of fatty acid biosynthetic process / endosome organization / cytoplasm protein quality control / protein K11-linked ubiquitination / protein K27-linked ubiquitination / protein quality control for misfolded or incompletely synthesized proteins / tertiary granule membrane / ficolin-1-rich granule membrane / specific granule membrane / Dengue virus activates/modulates innate and adaptive immune responses / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / positive regulation of autophagy / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / response to oxidative stress / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoskeleton / calmodulin binding / endosome / Neutrophil degranulation / nucleoplasm / zinc ion binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase UBR4, N-terminal / : / E3 ubiquitin-protein ligase UBR4 N-terminal / : / E3 ubiquitin-protein ligase UBR4-like domain / E3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 / UBR4 E3 catalytic module profile. / Putative zinc finger in N-recognin (UBR box) ...E3 ubiquitin-protein ligase UBR4, N-terminal / : / E3 ubiquitin-protein ligase UBR4 N-terminal / : / E3 ubiquitin-protein ligase UBR4-like domain / E3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 / UBR4 E3 catalytic module profile. / Putative zinc finger in N-recognin (UBR box) / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Armadillo-type fold / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase UBR4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsHu Z / Yan R
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Protein Cell / Year: 2026
Title: Structural and mechanistic insights into the UBR4-KCMF1-Calmodulin complex.
Authors: Ziwei Hu / Zhiheng Liu / Jiali Xu / Baotong Zhang / Renhong Yan /
History
DepositionNov 6, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66968.png

Downloads & links

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Map

FileDownload / File: emd_66968.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 520 pix.
= 430.04 Å		0.83 Å/pix.
x 520 pix.
= 430.04 Å		0.83 Å/pix.
x 520 pix.
= 430.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-4.3689795 - 3.7110732
Average (Standard dev.)-0.0011843642 (±0.022237668)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 430.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66968_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66968_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : N-terminal lobe of the human UBR4

EntireName: N-terminal lobe of the human UBR4
Components
  • Complex: N-terminal lobe of the human UBR4
    • Protein or peptide: E3 ubiquitin-protein ligase UBR4

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Supramolecule #1: N-terminal lobe of the human UBR4

SupramoleculeName: N-terminal lobe of the human UBR4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: E3 ubiquitin-protein ligase UBR4

MacromoleculeName: E3 ubiquitin-protein ligase UBR4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 185.453328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK SGPDEVDASG RATSGGEEAA AAAPAPGTPA TGADTTPGWE VAVRPLLSAS YSAFEMKELP QLVASVIESE SEILHHEKQ YEPFYSSFVA LSTHYITTVC SLIPRNQLQS VAAACKVLIE FSLLRLENPD EACAVSQKHL ILLIKGLCTG C SRLDRTEI ...String:
MADYKDDDDK SGPDEVDASG RATSGGEEAA AAAPAPGTPA TGADTTPGWE VAVRPLLSAS YSAFEMKELP QLVASVIESE SEILHHEKQ YEPFYSSFVA LSTHYITTVC SLIPRNQLQS VAAACKVLIE FSLLRLENPD EACAVSQKHL ILLIKGLCTG C SRLDRTEI ITFTAMMKSA KLPQTVKTLS DVEDQKELAS PVSPELRQKE VQMNFLNQLT SVFNPRTVAS QPISTQTLVE GE NDEQSST DQASAIKTKN VFIAQNVASL QELGGSEKLL RVCLNLPYFL RYINRFQDAV LANSFFIMPA TVADATAVRN GFH SLVIDV TMALDTLSLP VLEPLNPSRL QDVTVLSLSC LYAGVSVATC MAILHVGSAQ QVRTGSTSSK EDDYESDAAT IVQK CLEIY DMIGQAISSS RRAGGEHYQN FQLLGAWCLL NSLFLILNLS PTALADKGKE KDPLAALRVR DILSRTKEGV GSPKL GPGK GHQGFGVLSV ILANHAIKLL TSLFQDLQVE ALHKGWETDG PPAALSIMAQ STSIQRIQRL IDSVPLMNLL LTLLST SYR KACVLQRQRK GSMSSDASAS TDSNTYYEDD FSSTEEDSSQ DDDSEPILGQ WFEETISPSK EKAAPPPPPP PPPLESS PR VKSPSKQAPG EKGNILASRK DPELFLGLAS NILNFITSSM LNSRNNFIRN YLSVSLSEHH MATLASIIKE VDKDGLKG S SDEEFAAALY HFNHSLVTSD LQSPNLQNTL LQQLGVAPFS EGPWPLYIHP QSLSVLSRLL LIWQHKASAQ GDPDVPECL KVWDRFLSTM KQNALQGVVP SETEDLNVEH LQMLLLIFHN FTETGRRAIL SLFVQIIQEL SVNMDAQMRF VPLILARLLL IFDYLLHQY SKAPVYLFEQ VQHNLLSPPF GWASGSQDSN SRRATTPLYH GFKEVEENWS KHFSSDAVPH PRFYCVLSPE A SEDDLNRL DSVACDVLFS KLVKYDELYA ALTALLAAGS QLDTVRRKEN KNVTALEACA LQYYFLILWR ILGILPPSKT YI NQLSMNS PEMSECDILH TLRWSSRLRI SSYVNWIKDH LIKQGMKAEH ASSLLELAST TKCSSVKYDV EIVEEYFARQ ISS FCSIDC TTILQLHEIP SLQSIYTLDA AISKVQVSLD EHFSKMAAET DPHKSSEITK NLLPATLQLI DTYASFTRAY LLQN FNEEG TTEKPSKEKL QGFAAVLAIG SSRCKANTLG PTLVQNLPSS VQTVCESWNN INTNEFPNIG SWRNAFANDT IPSES YISA VQAAHLGTLC SQSLPLAASL KHTLLSLVRL TGDLIVWSDE MNPPQVIRTL LPLLLESSTE SVAEISSNSL ERILGP AES DEFLARVYEK LITGCYNILA NHADPNSGLD ESILEECLQY LEKQLESSQA RKAMEEFFSD SGELVQIMMA TANENLS AK FCNRVLKFFT KLFQLTEKSP NPSLLHLCGS LAQLACVEPV RLQAWLTRMT TSPPKDSDQL DVIQENRQLL QLLTTYIV R ENSQVGEGVC AVLLGTLTPM ATEMLANGDG TGFPELMVVM ATLASAGQGA GHLQLHNAAV DWLSRCKKYL SQKNVVEKL NANVMHGKHV MILECTCHIM SYLADVTNAL SQSNGQGPSH LSVDGEERAI EVDSDWVEEL AVEEEDSQAE DSDEDSLCNK LC

UniProtKB: E3 ubiquitin-protein ligase UBR4

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI MORGAGNI
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5625 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 244291
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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